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get_MIE_file

Read-only

Retrieve the MIE file for a specified RDF database to access its ShEx schema, RDF, and SPARQL examples before querying, ensuring correct SPARQL syntax and database structure.

Instructions

At the start of any task, identify ALL databases needed and call this tool for EACH of them before writing any SPARQL queries. Do not query a database until its MIE file has been read. Get the MIE (Metadata Interoperability Exchange) file containing the ShEx schema, RDF and SPARQL examples of a specific RDF database. RETURNS the MIE file as a YAML-formatted string; an unknown database returns a string beginning with 'Error:' that lists the valid database names.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
dbNoAlias for `database`.
dbnameNoAlias for `database`.
databaseNoName of a single RDF database. Must be exactly one of: uniprot, rhea, pubchem, pdb, chembl, chebi, reactome, ensembl, amrportal, mesh, go, taxonomy, mondo, nando, bacdive, mediadive, clinvar, pubmed, pubtator, ncbigene, medgen, ddbj, glycosmos, supercon, bgee, oma, brenda, hgnc, jpostdb, massbank, nbrc, mogplus, hco, mco, togovar, ontology, gwascatalog. Do NOT pass an endpoint group name here (e.g. 'ebi', 'sib') — those go in endpoint_name instead.

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault
resultYes
Behavior4/5

Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?

Annotations already signal read-only and open-world behavior, so the bar for additional disclosure is lower. The description adds concrete behavioral details: it returns a YAML-formatted string and an unknown database returns an error string listing valid database names. This goes beyond the annotations without contradicting them.

Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.

Conciseness5/5

Is the description appropriately sized, front-loaded, and free of redundancy?

The description is front-loaded with the most important usage instruction in bold, followed by a concise definition and return behavior. Every sentence contributes meaningful information, and there is no redundant repetition of schema details.

Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.

Completeness5/5

Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?

Given the output schema and fully documented parameters, the description provides the remaining context needed: when to call it, what it returns, and how errors are surfaced. It is complete for an agent selecting and invoking this tool correctly.

Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.

Parameters3/5

Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?

Schema description coverage is 100%, with each parameter fully documented including db/dbname as aliases and a detailed list of valid database values. The description adds no per-parameter semantics beyond what the schema already provides, so the baseline score of 3 is appropriate.

Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.

Purpose5/5

Does the description clearly state what the tool does and how it differs from similar tools?

The description clearly states the tool gets the MIE file for a specific RDF database, including its ShEx schema, RDF, and SPARQL examples. This specific verb-resource pairing and the explicit prerequisite to run before SPARQL queries distinguishes it from sibling tools like run_sparql.

Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.

Usage Guidelines5/5

Does the description explain when to use this tool, when not to, or what alternatives exist?

The description provides explicit workflow guidance: identify all databases needed and call this tool for each before writing any SPARQL queries. It also states when not to proceed ('Do not query a database until its MIE file has been read'), giving clear usage context.

Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.

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